Phylogenetic utility of 19 low copy nuclear genes in closely related genera and species of caesalpinioid legumes

Numerous studies have identified low copy nuclear genes (LCNG) with phylogenetic potential throughout angiosperms, several specifically focused on Leguminosae. However, phylogenetic resolution at the species- to subspecies-level is often inferred based only on a small subset of taxa scattered throughout the higher level study group. This study aims to reassess the phylogenetic resolution of 19 previously published nuclear regions in Leguminosae using 18 species from two clades of the Caesalpinieae representing both distantly related genera and closely related species. Nuclear regions were amplified and aligned throughout the sampled taxa. Sequences were cloned when polymorphism was noted. The plastid loci matK, rps16, trnL, trnD–trnT and the nuclear ribosomal ITS regions were also analyzed for comparison. Phylogenetic analyses using parsimony were performed on individual matrices. Three nuclear regions were eliminated due to the non-specificity of the primers (RNAH, PTSB, GI). Four regions showed lower resolution than predicted from previous studies (MMK1, CYB6, RBPCO, EFGC), while three revealed greater resolution than anticipated (SQD1, AT103, EIF3E). Three other markers indicated previously unidentified duplication events for the genus Caesalpinia s.l. (ATCP and AROB) and at the base of the Caesalpinia and Peltophorum clades (CALTL). Phylogenies reconstructed from the intron-spanning regions AIGP, SHMT, AT103 and EIF3E are congruent with ITS and plastid data and show the best phylogenetic potential for studies of closely related species of caesalpinioid legumes. We present a screening strategy for the evaluation of LCNG for phylogenetic studies.